Rational construction of compact de novo-designed biliverdin-binding proteins

Abstract: We report the rational construction of a de novo -designed biliverdin-binding protein by first principles of protein design, informed by energy minimization modeling in Rosetta. The self-assembling tetrahelical bundles bind biliverdin IXa (BV) cofactor auto-catalytically in vitro , similar to photosensory proteins that bind BV (and related bilins, or linear tetrapyrroles) despite lacking sequence and structural homology to the natural counterparts. Upon identifying a suitable site for cofactor ligation to the protein scaffold, stepwise placement of residues stabilized BV within the hydrophobic core. Rosetta modeling was used in the absence of a high-resolution structure to define the structure-function of the binding pocket. Holoprotein formation indeed stabilized BV, resulting in increased far-red BV fluorescence. By removing segments extraneous to cofactor stabilization or bundle stability, the initial 15-kilodalton de novo -designed fluorescence-activating protein (“dFP”) was truncated without altering its optical properties, down to a miniature 10-kilodalton “mini,” in which the protein scaffold extends only a half-heptad repeat beyond the hypothetical position of the bilin D-ring. This work demonstrates how highly compact holoprotein fluorochromes can be rationally constructed using de novo protein design technology and natural cofactors.