Cytochrome c oxidase: chemistry of a molecular machine

The plethora of proposed chemical models attempting to explain the proton pumping reactions catalyzed by the CcO complex, especially the number of recent models, makes it clear that the problem is far from solved. Although we have not discussed all of the models proposed to date, we have described some of the more detailed models in order to illustrate the theoretical concepts introduced at the beginning of this section on proton pumping as well as to illustrate the rich possibilities available for effecting proton pumping. It is clear that proton pumping is effected by conformational changes induced by oxidation/reduction of the various redox centers in the CcO complex. It is for this reason that the CcO complex is called a redox-linked proton pump. The conformational changes of the proton pump cycle are usually envisioned to be some sort of ligand-exchange reaction arising from unstable geometries upon oxidation/reduction of the various redox centers. However, simple geometrical rearrangements, as in the Babcock and Mitchell models are also possible. In any model, however, hydrogen bonds must be broken and reformed due to conformational changes that result from oxidation/reduction of the linkage site during enzyme turnover. Perhaps the most important point emphasized in this discussion, however, is the fact that proton pumping is a directed process and it is electron and proton gating mechanisms that drive the proton pump cycle in the forward direction. Since many of the models discussed above lack effective electron and/or proton gating, it is clear that the major difficulty in developing a viable chemical model is not formulating a cyclic set of protein conformational changes effecting proton pumping (redox linkage) but rather constructing the model with a set of physical constraints so that the proposed cycle proceeds efficiently as postulated. In our discussion of these models, we have not been too concerned about which electron of the catalytic cycle was entering the site of linkage, but merely whether an ET to the binuclear center played a role. However, redox linkage only occurs if ET to the activated binuclear center is coupled to the proton pump. Since all of the models of proton pumping presented here, with the exception of the Rousseau expanded model and the Wikström model, have a maximum stoichiometry of 1 H+/e-, they inadequately explain the 2 H+/e- ratio for the third and fourth electrons of the dioxygen reduction cycle (see Section V.B). One way of interpreting this shortfall of protons is that the remaining protons are pumped by an as yet undefined indirectly coupled mechanism. In this scenario, the site of linkage could be coupled to the pumping of one proton in a direct fashion and one proton in an indirect fashion for a given electron. For a long time, it was assumed that at least some elements of such an indirect mechanism reside in subunit III. While recent evidence argues against the involvement of subunit III in the proton pump, subunit III may still participate in a regulatory and/or structural capacity (Section II.E). Attention has now focused on subunits I and II in the search for residues intimately involved in the proton pump mechanism and/or as part of a proton channel. In particular, the role of some of the highly conserved residues of helix VIII of subunit I are currently being studied by site directed mutagenesis. In our opinion, any model that invokes heme alpha 3 or CuB as the site of linkage must propose a very effective means by which the presumedly fast uncoupling ET to the dioxygen intermediates is prevented. It is difficult to imagine that ET over the short distance from heme alpha 3 or CuB to the dioxygen intermediate requires more than 1 ns. In addition, we expect the conformational changes of the proton pump to require much more than 1 ns (see Section V.B).

DNA-mediated electron transfer from a modified base to ethidium: pi-stacking as modulator of reactivity

BACKGROUND

The DNA double helix is composed of an array of aromatic heterocyclic base pairs and, as a molecular pi-stack, represents a novel system for studying long-range electron transfer. Because many base damage and repair processes result from electron-transfer reactions, the ability of DNA to mediate charge transport holds important biological implications. Seemingly contradictory conclusions have been drawn about electron transfer in DNA from the many different studies that have been carried out. These studies must be reconciled so that this phenomenon can be understood both at a fundamental level and in the context of biological systems.

RESULTS

The photoinduced oxidation of a modified base, 7-deazaguanine, has been examined as a function of distance, sequence, and base stacking in DNA duplexes covalently modified with ethidium. Over ethidium/deazaguanine separations of 6-27 A, the photooxidation reaction proceeded on a subnanosecond time scale, and the quenching yield exhibited a shallow distance dependence. The efficiency of the reaction was highly sensitive to small changes in base composition. Moreover, the overall distance-dependence of the reaction is sensitive to sequence, despite the constancy of photoexcited ethidium as acceptor.

CONCLUSIONS

The remarkable efficiency of deazaguanine photooxidation by intercalated ethidium over long distances provides new evidence for fast electron-transfer pathways through DNA. By varying sequence as well as reactant separation, this work provides the first experimental demonstration of the importance of reactant stacking in the modulation of long-range DNA mediated electron transfer.

Determination of rate and equilibrium constants for the reactions between electron transfer mediators and proteins by linear sweep voltammetry

Redox proteins undergo measurable charge transfer at electrodes only under special circumstances, while they readily take part in electron transfer reactions with mediators in solution. Advantage was taken of the latter fact to develop a new method to study the kinetics and equilibria of protein-mediator electron transfer reactions. It was shown that rate and equilibrium constants for the electron exchange between electron transfer mediator and the protein can be obtained from the analysis of the perturbation of the linear sweep voltammetry (LSV) response of the mediator due to the presence of the protein. The experiments were carried out under conditions where the protein does not interact with the electrode. Theoretical data obtained by digital simulation are presented to show the conditions under which rate and equilibrium constants are accessible by the LSV technique. The electron transfer reactions between ferri- and ferrocytochrome c and N,N,N',N'-tetramethylphenylenediamine and the corresponding radical cation in phosphate-buffered saline (0.04 M phosphate, pH 7.4, 0.1 M NaCl) buffer were selected to demonstrate the technique. These studies resulted in an equilibrium constant equal to 1.0 and forward and reverse rate constants equal to 1.6 x 10(4) M-1 s-1. The data available from this method include forward and reverse rate constants for electron transfer and the formal potential for the protein redox couple.

Rate Constants for Charge Transfer Across Semiconductor-Liquid Interfaces

Interfacial charge-transfer rate constants have been measured for n-type Si electrodes in contact with a series of viologen-based redox couples in methanol through analyses of the behavior of these junctions with respect to their current density versus potential and differential capacitance versus potential properties. The data allow evaluation of the maximum rate constant (and therefore the electronic coupling) for majority carriers in the solid as well as of the dependence of the rate constant on the driving force for transfer of delocalized electrons from the n-Si semiconducting electrode into the localized molecular redox species in the solution phase. The data are in good agreement with existing models of this interfacial electron transfer process and provide insight into the fundamental kinetic events underlying the use of semiconducting photoelectrodes in applications such as solar energy conversion.