Threading a peptide through a peptide: protein loops, rotaxanes, and knots

Area of Science:

• Biochemistry
• Supramolecular Chemistry
• Chemical Biology

Background:

• Proteins naturally adopt complex folds, generally avoiding knotted or threaded conformations.
• The reasons for this avoidance are debated: fundamental folding barriers or evolutionary selection.
• Supramolecular chemistry has established methods for creating topological links in small molecules.

Purpose of the Study:

• To investigate the feasibility of synthesizing topologically linked protein complexes.
• To explore whether principles from small-molecule supramolecular chemistry can be applied to protein assembly.
• To determine if proteins can be intentionally threaded through cyclic structures.

Main Methods:

• Utilized principles of organic synthesis and supramolecular chemistry.
• Assembled a topologically linked protein complex by threading a linear protein through a cyclic protein, forming a [2]pseudo-rotaxane.
• Employed native chemical ligation to cyclize the linear protein, resulting in a [2]heterocatenane.

Main Results:

• Successfully demonstrated the assembly of a [2]heterocatenane using protein components.
• Showed that threading a linear protein through a cyclic protein is achievable.
• Observed that protein threading kinetics are slower than native protein folding kinetics but remain efficient.

Conclusions:

• It is possible to synthesize topologically linked protein complexes using established chemical principles.
• Protein threading is an efficient process, suggesting that proteins can be engineered into complex topological architectures.
• The findings challenge the notion that proteins inherently avoid threaded conformations due to fundamental barriers.