A Stevedore's protein knot.
Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered alpha-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified protein fragment that consists of only 92 amino acids. The topological complexity of the Stevedore knot presents a puzzle as to how it could possibly fold. To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possible mechanism by which the knot forms in a single loop flip.
Bölinger
Daniel
D
Department of Physics, Johannes Gutenberg-Universität Mainz, Mainz, Germany.
Sułkowska
Joanna I
JI
Hsu
Hsiao-Ping
HP
Mirny
Leonid A
LA
Kardar
Mehran
M
Onuchic
José N
JN
Virnau
Peter
P
D030562:Databases, Protein; D006867:Hydrolases / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D017510:Protein Folding
D006867:Hydrolases; C034507:2-haloacid dehalogenase