Remote control of synthetic knots through peptide sequences

The primary amino acid sequence dictates the structural, conformational and functional properties of proteins. Extending this sequence-function paradigm to synthetic self-assemblies provides a powerful means to program molecular structure and emergent properties with precision. Here, we report the remote control of both the stereoselective synthesis and functional properties of molecular cinquefoil knots by modification of the peptide sequence attached to the knotted loop. Specifically, six dipeptide chains, containing alanine (Ala), valine (Val) or phenylalanine (Phe) units, are incorporated directly into the ligand backbone at sites peripheral to the knotted core. Using a metal-templated approach followed by ring-closing metathesis, distinct knotted architectures were prepared with high efficiency (58%–95%) and complete stereoselectivity. Advanced NMR analyses confirmed that subtle sequence variations influence local conformational preferences without altering topological integrity. Heterogeneous peptide helicates display rapid exchange in self-sorting compared with their homogeneous counterparts, owing to steric and cooperative mismatches, resulting in reduced stability, reminiscent of sequence-dependent stabilization in protein folding and assembly. Circular dichroism studies demonstrated that global topology dominates the chiroptical response, with minor modulation from residue placement. UV-vis titrations revealed strong bromide binding (K_a > 10⁵ M⁻¹), with sequence-specific variations in affinity, highlighting the role of residue identity and position in modulating molecular recognition. Incorporation of a tripeptide sequence further demonstrated the broad applicability of the strategy. These results establish a general strategy for encoding functional information in molecular knots through peripheral amino acid sequences, providing a biomimetic means of remotely controlling the functions of topologically complex molecular architectures.