AlphaFold predicts the most complex protein knot and composite protein knots

Abstract

The computer artificial intelligence system AlphaFold has recently predicted previously unknown three-dimensional structures of thousands of proteins. Focusing on the subset with high-confidence scores, we algorithmically analyze these predictions for cases where the protein backbone exhibits rare topological complexity, that is, knotting. Amongst others, we discovered a 7₁ -knot, the most topologically complex knot ever found in a protein, as well several six-crossing composite knots comprised of two methyltransferase or carbonic anhydrase domains, each containing a simple trefoil knot. These deeply embedded composite knots occur evidently by gene duplication and interconnection of knotted dimers. Finally, we report two new five-crossing knots including the first 5₁ -knot. Our list of analyzed structures forms the basis for future experimental studies to confirm these novel-knotted topologies and to explore their complex folding mechanisms.

Keywords: AlphaFold; composite knots; protein knots; protein topology.

FIGURE 1

3D structure (top) and reduced representation (bottom) of a six‐crossing composite knot in protein Q313J9 (methyltransferase). A composite trefoil knot (3₁#3₁) can be identified. Topologically trivial segments are not displayed. Inset: A similar structure is predicted for Methyltransferase A4I142, except the two knotted domains form a more compact arrangement

FIGURE 2

3D structure (top) and reduced representation (bottom) of protein P54212 (carbonic anhydrase). A composite trefoil knot (3₁#3₁) can be identified. Topologically trivial segments are not displayed. The large green segments in the top structure are made transparent for a better view of the knotted region

FIGURE 3

Structure and topology of proteins P73136 (left) and Q9PR55 (right). Top: 3D structures predicted by AlphaFold. Bottom: Reduced representations to visualize the 5₁‐ and 7₁‐knots in the left and right structure, respectively. On the right, the dark blue segment introduces an additional winding

FIGURE 4

Structure and topology of proteins A0A0K0IQS9 (left) and C1GYM9 (right). Top: 3D structures predicted by AlphaFold. Bottom: Reduced representations to visualize the 5₁‐ and 5₂‐knots in the left and right structure, respectively