Abstract:

Protein design provides a platform to test principles of protein folding and function on a small, controlled scale. It also provides a means to create entirely new proteins with novel catalytic or biosensing functions. The design and characterization of a metal-assembled trimeric coiled coil protein that functions as a discriminatory receptor for small hydrophobic benzene and cyclohexane analogs is introduced here.

The trimeric coiled coil receptor protein [Fe(bpyGCN4-N16A)3 ] 2+ was designed based on the GCN4-p1 peptide sequence. A small hydrophobic cavity was introduced by substituting three core valine residues with smaller alanines. To overcome the difficulty of specifying oligomeric state, metal coordination was used to assemble the trimer. The stabilities of the designed proteins were confirmed by circular dichroism spectroscopy.

Several NMR experiments, including T1 relaxation, NOESY, and saturation transfer difference provided evidence that benzene was binding to [Fe(bpyGCN4-N16A) 3 ]2+ , but not to the control protein [Fe(bpyGCN4-N16V) 3 ]2+ . Because the two proteins were otherwise identical except in that [Fe(bpyGCN4-N16V)3 ]2+ lacked a cavity, this positively indicated that benzene was binding in the cavity of [Fe(bpyGCN4-16A) 3 ]2+ .

The KD of hexafluorobenzene binding to [Fe(bpyGCN4-N16A) 3 ]2+ obtained by pulsed field gradient spin echo NMR diffusion was 1.1(9) ? 10-4 M. Using hexafluorobenzene as a reference molecule, the binding constants of a variety of hydrophobic and hydrophilic benzene and cyclohexane analogs were calculated by a novel 19 F competitive inhibition assay introduced here. As expected, hydrophobic ligands bound in the hydrophobic cavity with higher affinity than hydrophilic ligands. In addition, the cavity was able to discriminate between molecules of similar hydrophobicity based on their relative sizes.

The design was extended to a tri-glycine cavity [Fe(bpyGCN4-N16G) 3 ]2+ . Using the same method for determining binding constants as for [Fe(bpyGCN4-N16A)3 ]2+ , it was discovered that the slightly larger tri-glycine cavity bound larger benzene and cyclohexane analogs more favorably than did [Fe(bpyGCN4-N16A)3 ]2+ . Thus, the cavity-containing [Fe(bpyGCN4)3 ]2+ constructs were sufficiently stable and well folded to be able to discriminate between similar molecules on the basis of complementary hydrophobicity, size, and packing interactions.