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We report on a comparative investigation of the heme pocket fields of two Zn-substituted c-type cytochromes-namely yeast and horse heart cytochromes c-using a combination of hole burning Stark spectroscopy and electrostatic calculations. The spectral hole burning experiments are consistent with different pocket fields experienced at the hemes of the respective cytochromes. In the case of horse heart Zn-cytochrome c, two distinguishable electronic origins with different electrostatic properties are observed. The yeast species, on the other hand, displays a single electronic origin. Electrostatic calculations and graphics modeling using the linearized finite-difference Poisson-Boltzmann equation performed at selected time intervals on nanosecond-molecular dynamics trajectories show that the hemes of the respective cytochromes sample different potentials as they explore conformational space. The electrostatic potentials generated by the protein matrix at the heme show different patterns in both cytochromes, and we suggest that the cytochromes differ by the number of "electrostatic substates" that they can sample, thus accounting for the different spectral populations observed in the two cytochromes.

Mg-mesoporphyrin horseradish peroxidase (MgMP-HRP) and MgMP-HRP complexed with naphtohydroxamic acid (NHA) have been studied by fluorescence line narrowing (FLN) and pressure tuning spectral hole burning (SHB) techniques. In each sample, the low temperature absorption spectra show more than one transition in the origin range of the Q band. Comparisons with broad-band fluorescence spectra and FLN studies suggest that the multiple band feature originates from the presence of different configurations of the metal-porphyrin that are subject to Qx-Qy splitting within the protein cavity. This suggestion is supported by pressure tuning SHB studies. In the uncomplexed as well as in the NHA-complexed form of MgMP-HRP, irradiation in the Q band produces photoproduct bands, which has been attributed to a species with smaller Qx-Qy splitting. In an amorphous matrix, on the other hand, only one form of MgMP could be found, and no splitting could be observed. The binding of NHA does not significantly alter the bulk parameters of the protein matrix, but it reduces the structural variety in the configuration of MgMP to a single form with a more distorted structure and thus with an enlarged Qx-Qy splitting.

We performed hole-burning Stark effect experiments on cytochrome c in which the iron of the herne was either removed or replaced by Zn. According to the experiments, the free-base compound has an effective inversion center, even in the protein. The Zn compound, on the other hand, shows quite peculiar features: in the low-frequency range of the inhomogeneous band, it definitely has a dipole moment, as indicated by a splitting of the hole in the external field. However, in the maximum of the inhomogeneous band, a severe charge redistribution occurs, as the experiments show. In addition to the Stark experiments, we performed calculations of the electrostatic fields at the pyrrole rings and at the metal site of the heme group. We interpret our findings with a model based on structural hierarchies: the protein can exist in a few subconformations, which can be distinguished through the structure of the heme pocket. The different pocket structures support different structures of the chromophore, which, in turn, can be distinguished through their behavior in an external field. These distinct structures, in turn, correspond to a rather broad distribution of protein structures, which leave, however, the pocket structure largely unchanged. These structures show up in inhomogeneous broadening.

To clarify the role of metal ion coordination in horseradish peroxidase C (HRPC), the effect of pressure and of an externally applied electric field on spectral holes was compared for both metal-free and Mg-mesoporphyrin-substituted horseradish peroxidase C (MP-HRP and MgMP-HRP), as affected by the binding of 2-naphthohydroxamic acid (NHA). The data are compared to earlier studies performed on the same derivatives. Results obtained for MP-HRP show the presence of a predominant MP tautomer, as well as that of another small population with different pocket field and isothermal compressibility (0.12 vs 0.24 GPa(-1)). Binding NHA induces the formation of two new almost equal populations of MP-HRP tautomer complexes and the protein compressibility in both forms is increased to 0.50 and 0.36 GPa(-1). The protein structure becomes much softer than in the absence of NHA. Binding the same substrate to MgMP-HRP resulted in MgMP adopting a single conformation with no compressibility changes, while without NHA, two forms were possible. Stark effect results show charge rearrangement upon substrate binding in both cases. We propose that it is the presence of the metal that stabilizes the structure during the reorganization of the protein matrix induced by the substrate binding event. With the metal, only one conformation is adopted, without significant structural rearrangement but with charge redistribution. The dissociation constants determined for NHA binding to both derivatives and to native HRPC show that studies using mesoporphyrin and Mg-mesoporphyrin derivatives are relevant to investigating the specificity of the substrate-binding pocket in this enzyme.