Science 338, 783–785(2012)

Knotted proteins are relatively common, but synthesizing intertwined chemical structures is extremely challenging because it requires precise synthetic steps that bypass more readily accessible macrocycles. Now, Jeremy Sanders and colleagues at the University of Cambridge and the University of Bath have created a molecule that can self-assemble into a trefoil knot.

The molecule is composed of three naphthalene diimides, which are held together by flexible alanine linkers and are terminated at both ends with a cysteine amino acid. In water, the thiol groups of the cysteine ends oxidize to form disulphide bonds. The reaction can lead to the formation of cyclic monomers, dimers and trimers, and by increasing the polarity of the solution (that is, by adding a salt) the trimer is the preferred product. The researchers found that the trimer has a short retention time in a liquid chromatography column, eluting between the cyclic monomer and the cyclic dimer. This is a clear indication that some hydrophobic parts of the molecule are buried within the structure so as to avoid contact with water and maximize hydrophobic interactions. The knotted structure was confirmed by nuclear magnetic resonance spectroscopy and the chirality of the knot can be controlled by the handedness of the peptide linkers.

The molecular structure of the precursor — three hydrophobic, electron-deficient units linked by short, flexible hydrophilic linkers — could be a general strategy for achieving knotted structures by self-assembly and might also represent a model system for studying knot formation in proteins.