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    J Am Chem Soc. 2005 Feb 9;127(5):1346-7.

    Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor.

    Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF.

    Department of Biochemistry and Molecular Biophysics, Johnson Foundation, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

    Erratum in:

    • J Am Chem Soc. 2006 Jan 18;128(2):663.

    We report the complete de novo design of a four-helix bundle protein that selectively binds the nonbiological DPP-Fe(III) metalloporphyrin cofactor (DPP-Fe(III) = 5, 15-Di[(4-carboxymethyleneoxy)phenyl]porphinato iron(III)). A tetrameric, D2-symmetric backbone scaffold was constructed to encapsulate two DPP-Fe(III) units through bis(His) coordination. The complete sequence was determined with the aid of the statistical computational design algorithm SCADS. The 34-residue peptide was chemically synthesized. UV-vis and CD spectroscopy, size-exclusion chromatography, and analytical ultracentrifugation indicated the peptide undergoes a transition from a predominantly random coil monomer to an alpha-helical tetramer upon binding DPP-Fe(III). EPR spectroscopy studies indicated the axial imidazole ligands were oriented in a perpendicular fashion, as defined by second-shell interactions that were included in the design. The 1-D 1H NMR spectrum of the assembled protein displayed features of a well-packed interior. The assembled protein possessed functional redox properties different from those of structurally similar systems containing the heme cofactor. The designed peptide demonstrated remarkable cofactor selectivity with a significantly weaker binding affinity for the natural heme cofactor. These findings open a path for the selective incorporation of more elaborate cofactors into designed scaffolds for constructing molecularly well-defined nanoscale materials.

    PMID: 15686346 [PubMed - indexed for MEDLINE]

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