Heme proteins protein scaffolds

Local charge compensation of the formally charged Fe(III) heme, as discussed more fully in a later section, demonstrates a significant modulation (s 210 mV) of the heme reduction potential in a designed heme protein. This scaffold-dependent effect has been shown to be additive to the heme-dependent effect of porphyrin peripheral architecture to demonstrate the modulation of a designed heme protein reduction potential by 450 mV using a single maquette scaffold. 

These minimalistic peptide scaffolds potentially provide a biologically relevant laboratory in which to explore the details of heme-peptide interactions and, with development, perhaps approach the observed range of natural heme protein fimction. These heme-peptide systems are more complex than typical small molecule bioinorganic porphyrin model compoimds, and yet are seemingly not as enigmatic as even the smallest natural heme proteins. Thus, in the continuum of heme protein model complexes these heme-peptide systems lie closer to, but certainly not at, the small molecule limit which allows for the effects of single amino acid changes to be directly elucidated. 

Two reports in 1994 began to develop the concepts of coordination chemistry based self-assembly of heme into designed protein scaffolds. In collaborative work, the laboratories of DeGrado and Dutton provided two related architectures for de novo heme protein design... 

Monomeric hemes possess a mirror plane and are hence achiral (151). Incorporation of the heme macrocycle into the anisotropic protein matrix distorts the heme environment, inducing a circular dichroism spectrum (57, 152, 153). From the design standpoint, the presence of an induced heme CD spectrum qualitatively confirms intimate communication between the heme and the surrounding protein matrix, which indicates the heme is most likely specifically bound. This spectroscopic signature serves as a first indication that the heme resides within the designed protein scaffold and has been used by various groups to... 

The first general principle is that the type of metalloporphyrin incorporated into a designed protein or natural cytochrome offers a method to adjust the reduction potential of the heme. Sharp et al. (149) have demonstrated that a synthetic heme, l-methyl-2-oxomesoheme XIII, incorporated into a designed heme protein has a reduction potential 90 mV higher than the same protein with heme b. Additionally, Gib-ney et al. (148) have illustrated that heme a has a reduction potential 160 mV higher than heme b in the identical protein scaffold. This heme-dependent effect provides protein designers with a predictable modulation of the heme reduction potential in a synthetic protein. 

A rich source of potential industrial biocatalysts, the heme enzymes are also a superb testing ground for laboratory evolution. Directed evolution approaches are already generating customized heme enzymes and probing the limits of heme enzyme catalysis. Over the next few years, these same approaches will allow us to explore the interconversion of function among different protein scaffolds and thereby observe how the protein modulates heme chemistry and how new functions are acquired. 

B. Redesign of Nonheme Iron Proteins. In heme protein redesign described above, the heme prosthetic group largely dictates the active site structure. Redesign focuses mainly on the proximal and distal sides of the heme, causing minimal effects on the overall protein scaffolds. This is not necessarily the case for nonheme metalloproteins in which metal sites are not as dominant and small changes may have more dramatic effects on the protein folds and stability. 

FIGURE 22.18 Model of the R. viridis reaction center, (a, b) Two views of the ribbon diagram of the reaction center. Mand L subunits appear in purple and blue, respectively. Cytochrome subunit is brown H subunit is green. These proteins provide a scaffold upon which the prosthetic groups of the reaction center are situated for effective photosynthedc electron transfer. Panel (c) shows the spatial relationship between the various prosthetic groups (4 hemes, P870, 2 BChl, 2 BPheo, 2 quinones, and the Fe atom) in the same view as in (b), but with protein chains deleted. 

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