Resonance Raman evidence for low-spin Fe2+ heme a3 in energized cytochrome c oxidase: implications for the inhibition of O2 reduction

Exploring the structure and formation mechanism of amyloid fibrils by Raman spectroscopy: a review

Amyloid fibrils are β-sheet rich protein aggregates that are strongly associated with various neurodegenerative diseases. Raman spectroscopy has been broadly utilized to investigate protein aggregation and amyloid fibril formation and has been shown to be capable of revealing changes in secondary and tertiary structures at all stages of fibrillation. When coupled with atomic force (AFM) and scanning electron (SEM) microscopies, Raman spectroscopy becomes a powerful spectroscopic approach that can investigate the structural organization of amyloid fibril polymorphs. In this review, we discuss the applications of Raman spectroscopy, a unique, label-free and non-destructive technique for the structural characterization of amyloidogenic proteins, prefibrilar oligomers, and mature fibrils.

Deep UV Resonance Raman Spectroscopy for Characterizing Amyloid Aggregation

Deep UV resonance Raman spectroscopy is a powerful technique for probing the structure and formation mechanism of protein fibrils, which are traditionally difficult to study with other techniques owing to their low solubility and noncrystalline arrangement. Utilizing a tunable deep UV Raman system allows for selective enhancement of different chromophores in protein fibrils, which provides detailed information on different aspects of the fibrils' structure and formation. Additional information can be extracted with the use of advanced data treatment such as chemometrics and 2D correlation spectroscopy. In this chapter we give an overview of several techniques for utilizing deep UV resonance Raman spectroscopy to study the structure and mechanism of formation of protein fibrils. Clever use of hydrogen-deuterium exchange can elucidate the structure of the fibril core. Selective enhancement of aromatic amino acid side chains provides information about the local environment and protein tertiary structure. The mechanism of protein fibril formation can be investigated with kinetic experiments and advanced chemometrics.

Redox interactions in cytochrome c oxidase: from the "neoclassical" toward "modern" models

Because of recent experimental data on the redox characteristics of cytochrome c oxidase and renewed interest in the role of cooperativity in energy coupling, the question of redox cooperativity in cytochrome c oxidase is reexamined. Extensive redox cooperativity between more than two redox centers, some of which are spectrally invisible, may be expected for this electron transfer coupled proton pump. Such cooperativity, however, cannot be revealed by the traditional potentiometric experiments based on a difference in absorbance between two wavelengths. Multiwavelength analyses utilizing singular value decomposition and second derivatives of absorbance vs. wavelength have revealed a stronger cooperativity than consistent with the "neoclassical" model, which allowed only for weak negative cooperativity between two equipotential one-electron centers. A thermodynamic analysis of redox cooperativity is developed, which includes the possibilities of strong cooperative redox interactions, the involvement of invisible redox centers, conformational changes, and monomer/dimer equilibrations. The experimental observation of an oxidation of one of the cytochromes (a3) with a decrease in applied redox potential is shown to require both strong negative cooperativity and the participation of more than two one-electron centers. A number of "modern" models are developed using the analytical approaches described in this paper. By testing with experimental data, some of these models are falsified, whereas some are retained with suggestions for further testing.

Respiratory control in cytochrome oxidase vesicles is correlated with the rate of internal electron transfer

Cytochrome c oxidase, after reconstitution into phospholipid vesicles, displays respiratory control. This appears as an inhibition of substrate oxidation (cytochrome c) or reduction (O2) rates which, in the first few turnovers, can be largely removed upon addition of valinomycin, a specific K+ carrier. We report experiments designed to measure directly the internal electron transfer leading to the reduction of cytochrome a3/CuB, in the presence and the absence of a membrane potential. The results suggest that, after the complete oxidation and partial re-reduction of the protein, electron transfer to the binuclear site is valinomycin-sensitive, i.e. is inhibited by the membrane potential. The first-order rate constants calculated in the absence and presence of valinomycin were 0.5-0.6 and 5-6 s-1 respectively. Kinetic analysis of the reduction process is consistent with the conclusion that the membrane potential is below the critical threshold until the first electron is transferred to the cytochrome a3/CuB site. Furthermore, the respiratory control ratio obtained from the dependence of the internal electron transfer rate constant on valinomycin is always higher (by factor of 2) than that measured under turnover conditions either polarographically or spectrophotometrically. Two possible interpretations of this discrepancy are discussed.

Resolution of the electronic transitions of cytochrome c oxidase: evidence for two conformational states of ferrous cytochrome alpha

Second-derivative absorption spectra are reported for a variety of oxidation and ligation states of bovine cytochrome c oxidase (ferrocytochrome-c:oxygen oxidoreductase, EC 1.9.3.1). The high resolving power of the second-derivative method allows us to assign the individual electronic transitions of cytochrome alpha and cytochrome alpha 3 in many of these states. In the fully reduced enzyme, one observes a single electronic transition at 444 nm, corresponding to the Soret transition for both ferrous cytochrome alpha and ferrous cytochrome alpha 3. When the cytochrome alpha 3 site is occupied by an exogenous ligand (CN or CO), one observes two absorption bands assignable to the ferrous cytochrome alpha chromophore, one at ca, 443 nm and the other at ca, 450 nm. The appearance of the 450-nm band is dependent only on ligand occupancy at the cytochrome alpha 3 site and not on the oxidation state of the cytochrome alpha 3 iron. These results can be interpreted either in terms of a heterogeneous mixture of two ferrous cytochrome alpha conformers in the cytochrome alpha 3-ligated enzyme or in terms of a reduction in the effective molecular symmetry of the ferrous cytochrome alpha site that results in a lifting of the degeneracy of the lowest unoccupied molecular orbital associated with the Soret pi,pi* transition of cytochrome alpha. In either case, the present data indicate that ferrous cytochrome alpha can adopt two distinct conformations. One possible structural difference between these two states could be related to differences in the strength of hydrogen bonding between the ferrous cytochrome alpha formyl oxygen and a proton donor from an unidentified amino acid side chain of the enzyme. The implications of such modulation of hydrogen-bond strength are discussed in terms of possible mechanisms of proton translocation and electron transfer in the enzyme.

Nature and functional implications of the cytochrome a3 transients after photodissociation of CO-cytochrome oxidase

Time-resolved electronic absorption, infrared, resonance Raman, and magnetic circular dichroism spectroscopies are applied to characterization of the intermediate that is formed within 20 ps after photodissociation of CO from cytochrome a3 in reduced cytochrome oxidase. This intermediate decays with the same half-life (approximately 1 microseconds) as the post-photodissociation CU+B-CO species previously observed by time-resolved infrared. The transient UV/visible spectra, kinetics, infrared, and Raman evidence suggest that an endogenous ligand is transferred from CuB to Fea3 when CO binds to CuB, forming a cytochrome a3 species with axial ligation that differs from the reduced unliganded enzyme. The time-resolved magnetic circular dichroism results suggest that this transient is high-spin and, therefore, five-coordinate. Thus we infer that the ligand from CuB binds on the distal side of cytochrome a3 and displaces the proximal histidine imidazole. This remarkable mechanistic feature is an additional aspect of the previously proposed "ligand-shuttle" activity of the CuB/Fea3 pair. We speculate as to the identity of the ligand that is transferred between CuB and Fea3 and suggest that the ligand shuttle may play a functional role in redox-linked proton translocation by the enzyme.