(272i) Computational Design of a Single-Chain Four-Helix Bundle Protein with a Non-Biological Ru(II)Polypyridyl-(Porphinato)Zn(II) Cofactor

Combining proteins with non-biological cofactors holds great potential for the development of new materials. One example is a potential protein complex containing a Ru(II)polypyridyl-(porphinato)Zn(II) [Ru-PZn] cofactor, which shows substantial dynamic hyperpolarizability. This translates into a potential use of these cofactors in optoelectronic or light harvesting devices for the effective conversion of photonic energy into electrochemical potential energy. Possible applications are waveguide switches, modulators, filters, and polarization transformers. The protein should serve as a scaffold to align the Ru-PZn cofactor in a desired matrix, and to render it water-soluble. Previously, a four-helix bundle was designed, that selectively binds a non-biological Fe(III)-porphyrin [PFe] cofactor(1). This de-novo protein design utilizes the bis-His-based six-point coordination motif for the Fe3+ ion, which is naturally found in cytochrome bc1.

Here, we present a de-novo designed protein that is intended to bind the Ru-PZn cofactor. While this new design draws on experiences from the earlier project and also uses a four-helix bundle topology, it differs significantly from the earlier project. Through introducing loops that were found by superimposing loops from PDB structures onto the four-helix bundle, the backbone structure is transformed from a tertramer into a single polypeptide chain, which should facilitate easier handling of the protein-cofactor complex when subsequently aligning it in a two- or three-dimensional matrix. Furthermore, the 6-point coordination of the PFe design is reduced to a 5-point coordination in the Ru-PZn design. We discuss how the Statistical Computationally Assisted Design Strategy (SCADS)(2) was used to arrive at the final peptide sequence and present preliminary experimental results.

(1) FV Cochran, SP Wu, W Wang, V Nanda, JG Saven, MJ Therien, WF DeGrado; Journal of the American Chemical Society 127 (2005) 1346-47.

(2) H Kono, JG Saven; Journal of Molecular Biology 306 (2001) 607-28.