Computational Design and Elaboration of a De Novo Heterotetrameric α-Helical Protein that Selectively Binds an Emissive Abiological (Porphinato)zinc Chromophore

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Departmental Papers (Chemistry)
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Absorption
Amino Acid Sequence
Circular Dichroism
Computer Simulation
Drug Design
Electrons
Metalloporphyrins
Models, Molecular
Molecular Sequence Data
Peptides
Protein Multimerization
Protein Structure, Quaternary
Protein Structure, Secondary
Proteins
Substrate Specificity
Ultracentrifugation
Zinc
Absorption
Amino Acid Sequence
Circular Dichroism
Computer Simulation
Drug Design
Electrons
Metalloporphyrins
Models
Molecular
Molecular Sequence Data
Peptides
Protein Multimerization
Protein Structure
Quaternary
Protein Structure
Secondary
Proteins
Substrate Specificity
Ultracentrifugation
Zinc
Biochemistry
Organic Chemistry
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Abstract

The first example of a computationally de novo designed protein that binds an emissive abiological chromophore is presented, in which a sophisticated level of cofactor discrimination is pre-engineered. This heterotetrameric, C(2)-symmetric bundle, A(His):B(Thr), uniquely binds (5,15-di[(4-carboxymethyleneoxy)phenyl]porphinato)zinc [(DPP)Zn] via histidine coordination and complementary noncovalent interactions. The A(2)B(2) heterotetrameric protein reflects ligand-directed elements of both positive and negative design, including hydrogen bonds to second-shell ligands. Experimental support for the appropriate formulation of (DPP)Zn:A(His):B(Thr) is provided by UV/visible and circular dichroism spectroscopies, size exclusion chromatography, and analytical ultracentrifugation. Time-resolved transient absorption and fluorescence spectroscopic data reveal classic excited-state singlet and triplet PZn photophysics for the A(His):B(Thr):(DPP)Zn protein (k(fluorescence) = 4 x 10(8) s(-1); tau(triplet) = 5 ms). The A(2)B(2) apoprotein has immeasurably low binding affinities for related [porphinato]metal chromophores that include a (DPP)Fe(III) cofactor and the zinc metal ion hemin derivative [(PPIX)Zn], underscoring the exquisite active-site binding discrimination realized in this computationally designed protein. Importantly, elements of design in the A(His):B(Thr) protein ensure that interactions within the tetra-alpha-helical bundle are such that only the heterotetramer is stable in solution; corresponding homomeric bundles present unfavorable ligand-binding environments and thus preclude protein structural rearrangements that could lead to binding of (porphinato)iron cofactors.

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2010-03-24
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Journal of the American Chemical Society
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