Design of a functional protein for molecular recognition: specificity of ligand binding in a metal-assembled protein cavity probed by 19f NMR

A metal-assembled homotrimeric coiled coil based on the GCN4-p1 sequence has been designed that noncovalently binds hexafluorobenzene and other similar ligands in a hydrophobic cavity, created by making the core substitution Asn16Ala (Fe(bpyGCN4-N16A)3]2+). The KD of binding of hexafluorobenzene with Fe(bpyGCN4-N16A)3]2+ was observed to be 1.1(9) x 10(-4) M by diffusion NMR experiments. A control coiled coil with the core substitution Asn16Val (Fe(bpyGCN4-N16V)3]2+) exhibited a significantly weaker association with hexafluorobenzene, providing evidence that even in the absence of structural data, benzene-like ligands bind in the cavity created by the Asn16Ala substitution. 19F NMR was employed to observe hexafluorobenzene binding and to monitor titrations with competing hydrophobic and polar ligands similar in size and shape to hexafluorobenzene. All hydrophobic ligands bound with greater affinity than the polar ligands in the hydrophobic core, although the cavity seems to be somewhat flexible in terms of the sizes of molecules it can accommodate. Thus 19F NMR has proved to be a useful spectral tool to probe molecular recognition in a hydrophobic cavity of a metal-assembled coiled coil.