The Reorganization Energy of Cytochrome c Revisited

Abstract

The solution structures of the reduced and oxidized forms of the cytochrome c are used to reevaluate the reorganization energy for oxidation of cytochrome c. This is achieved by using the linear response approximation in concert with the NMR structures as pseudo energy constraints. Alternative estimates, obtained using a free energy perturbation approach employing umbrella sampling and a continuum dielectric approach, are also provided. The reorganization energy obtained is larger than that previously estimated using crystal structures of the protein. Nevertheless, the present estimate remains significantly smaller than the corresponding reorganization energy in water (9−15 kcal mol-1 as compared to ≈37 kcal mol-1 in water) and the protein contribution to the reorganization energy is only 8−10 kcal mol-1. This provides further support for the proposal that proteins assist in electron transfer reactions by reducing the relevant reorganization energies. The solution structures are also used to estimate the redox potential of cytochrome c. Several strategies are employed including a newly formulated scaled linear response approximation. The calculations agree reasonably well with the observed redox potential. Analysis of the group contributions to the reorganization energy and redox potential reveals a clear energetic linkage between these fundamental parameters of electron transfer and a redox-dependent surface feature likely to influence recognition of cytochrome c by its redox partners. Specifically, the rearrangement of Ile81 and other residues at the heme edge upon a change in oxidation state gives rise to a large contribution to both the redox potential and the reorganization energy. Finally this work is used to explore and illustrate the meaning of macroscopic dielectric models. It is shown that the “proper” dielectric constant depends strongly on the model used since it basically represents the implicit contributions of the given model rather than a fundamental physics. Thus we obtain different effective dielectric constants for different treatments of redox potential and reorganization energy.

Dielectric relaxation of cytochrome c oxidase: Comparison of the microscopic and continuum models

“…35. The distribution of titratable residues for our model of CcO is close to that for the "ionized" protein model 47 of cytochrome c for which the estimation p = 2.9 remarkably correlates with our result.…”

“…Indeed, matching ⌬G MD rf to the continuum free energy yields p = 1.3 for the dry CcO ͑see above subsection͒, which is unphysically low for the static dielectric constant for a condensed phase; indeed, it is even lower than pure electronic polarizability el ϳ 2. In contrast, MDEC approach leads to physically reasonable estimations that are in line with results of other authors 47 ͑see Sec. IV͒.…”

Ligand Dynamics in an Electron Transfer Protein

“…c the heme group is surrounded by a hydrophobic and relatively rigid pocket (12,13), and the protein contribution to the reorganization energy of cyt. c is thought to be weak (14,15). Structural flexibility is not advantageous for that function.…”

Electrostatic Environment of Hemes in Proteins: pKas of Hydroxyl Ligands

“…For example, sixcoordinate bis-His-hemes have E m s ranging from -410 to +360 mV with the redox differences being predominately due to the intraprotein electrostatic environment (1,(20)(21)(22). In these proteins the loss of solvation energy (15,23,24), interactions with the protein backbone and with other residues (15,(20)(21)(22)25), and local conformation changes on ionization changes (20,26) determine the thermodynamic equilibrium measured by pK a s and E m s.…”