Structure of a Zinc Porphyrin-Substituted Bacterioferritin and Photophysical Properties of Iron Reduction.

The iron storage protein bacterioferritin (Bfr) binds up to 12 hemes b at specific sites in its protein shell. The heme b can be substituted with the photosensitizer Zn(II)-protoporphyrin IX (ZnPP), and photosensitized reductive iron release from the ferric oxyhydroxide {[FeO(OH)]n} core inside the ZnPP-Bfr protein shell was demonstrated [Cioloboc, D., et al. (2018) Biomacromolecules 19, 178-187]. This report describes the X-ray crystal structure of ZnPP-Bfr and the effects of loaded iron on the photophysical properties of the ZnPP. The crystal structure of ZnPP-Bfr shows a unique six-coordinate zinc in the ZnPP with two axial methionine sulfur ligands. Steady state and transient ultraviolet-visible absorption and luminescence spectroscopies show that irradiation with light overlapping the Soret absorption causes oxidation of ZnPP to the cation radical ZnPP•+ only when the ZnPP-Bfr is loaded with [FeO(OH)]n. Femtosecond transient absorption spectroscopy shows that this photooxidation occurs from the singlet excited state (1ZnPP*) on the picosecond time scale and is consistent with two oxidizing populations of Fe3+, which do not appear to involve the ferroxidase center iron. We propose that [FeO(OH)]n clusters at or near the inner surface of the protein shell are responsible for ZnPP photooxidation. Hopping of the photoinjected electrons through the [FeO(OH)]n would effectively cause migration of Fe2+ through the inner cavity to pores where it exits the protein. Reductive iron mobilization is presumed to be a physiological function of Bfrs. The phototriggered Fe3+ reduction could be used to identify the sites of iron mobilization within the Bfr protein shell.

Switching protein metalloporphyrin binding specificity by design from iron to fluorogenic zinc.

Metalloporphyrins play important roles in areas ranging from biology to nanoscience. Using computational design, we converted metalloporphyrin specificity of cytochrome b562 from iron to fluorogenic zinc. The new variant had a near total preference for zinc representing a switch in specificity, which greatly enhanced the negligible aqueous fluorescence of free ZnPP in vitro and in vivo.

Structural, Photophysical, and Photochemical Characterization of Zinc Protoporphyrin IX in a Dimeric Variant of an Iron Storage Protein: Insights into the Mechanism of Photosensitized H2 Generation.

Some of us have previously reported the preparation of a dimeric form of the iron storage protein, bacterioferritin (Bfr), in which the native heme b is substituted with the photosensitizer, Zn(II)-protoporphyrin IX (ZnPP-Bfr dimer). We further showed that the ZnPP-Bfr dimer can serve as a photosensitizer for platinum-catalyzed H2 generation in aqueous solution without the usually added electron relay between photosensitizer and platinum ( Clark , E. R. , Inorg. Chem. 2017 , 56 , 4584 - 4593 ). We proposed reductive or oxidative quenching pathways involving the ZnPP anion radical (ZnPP•-) or the ZnPP cation radical, (ZnPP•+), respectively. The present report describes structural, photophysical, and photochemical properties of the ZnPP in the ZnPP-Bfr dimer. X-ray absorption spectroscopic studies at 10 K showed a mixture of five- and six-coordinated Zn centers with axial coordination by one long Zn-SγMet distance of ∼2.8 Å and ∼40% having an additional shorter Zn-S distance of ∼2.4 Å, in addition to the expected 4 nitrogen atom coordination from the porphyrin. The ZnPP in ZnPP-Bfr dimer was prone to photosensitized oxidation to ZnPP•+. The ZnPP•+ was rapidly reduced by ascorbic acid, which we previously determined was essential for photosensitized H2 production in this system. These results are consistent with an oxidative quenching pathway involving electron transfer from 3ZnPP* to platinum, which may be assisted by a flexible ZnPP axial coordination sphere. However, the low quantum yield for H2 production (∼1%) in this system could make reductive quenching difficult to detect, and can, therefore, not be completely ruled out. The ZnPP-Bfr dimer provides a simple but versatile framework for mechanistic assessment and optimization of porphyrin-photosensitized H2 generation without an electron relay between porphyrin and the platinum catalyst.

Photoinduced electron transfer within supramolecular hemoprotein co-assemblies and heterodimers containing Fe and Zn porphyrins.

Electron transfer (ET) events occurring within metalloprotein complexes are among the most important classes of reactions in biological systems. This report describes a photoinduced electron transfer between Zn porphyrin and Fe porphyrin within a supramolecular cytochrome b562 (Cyt b562) co-assembly or heterodimer with a well-defined rigid structure formed by a metalloporphyrin-heme pocket interaction and a hydrogen-bond network at the protein interface. The photoinduced charge separation (CS: kCS = 320-600 s-1) and subsequent charge recombination (CR: kCR = 580-930 s-1) were observed in both the Cyt b562 co-assembly and the heterodimer. In contrast, interestingly, no ET events were observed in a system comprised of a flexible and structurally-undefined co-assembly and heterodimers which lack the key hydrogen-bond interaction at the protein interface. Moreover, analysis of the kinetic constants of CS and CR of the heterodimer using the Marcus equation suggests that a single-step ET reaction occurs in the system. These findings provide strong support that the rigid hemoprotein-assembling system containing an appropriate hydrogen-bond network at the protein interface is essential for monitoring the ET reaction.

Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme.

Three paths for obtaining crystals of reduced (II-E4Q/I-K258R) cytochrome ba(3) are described, and the structures of these are reported at approximately 2.8-3.0 A resolution. Microspectrophotometry of single crystals of Thermus ba(3) oxidase at 100 K was used to show that crystals of the oxidized enzyme are reduced in an intense X-ray (beam line 7-1 at the Stanford Synchrotron Radiation Laboratory), being nearly complete in 1 min. The previously reported structures of ba(3) (Protein Data Bank entries 1EHK and 1XME ), having a crystallographically detectable water between the Cu(B) and Fe(a3) metals of the dinuclear center, actually represent the X-ray radiation-reduced enzyme. Dithionite-reduced crystals or crystals formed from dithionite-reduced enzyme revealed the absence of the above-mentioned water and an increase in the Cu(B)-Fe(a3) distance of approximately 0.3 A. The new structures are discussed in terms of enzyme function. An unexpected optical absorption envelope at approximately 590 nm is also reported. This spectral feature is tentatively thought to arise from a five-coordinate, low-spin, ferrous heme a(3) that is trapped in the frozen crystals.

Glycinebetaine protects the D1/D2/Cytb559 complex of photosystem II against photo-induced and heat-induced inactivation.

The presence of 1.0 mol/L glycinebetaine during isolation of D1/D2/Cytb559 reaction centre (RC) complexes from photosystem II (PSII) membrane fragments preserved the photochemical activity, monitored as the light-induced reduction of pheophytin and electron transport from diphenylcarbazide to 2.6-dichlorophenol-indophenol.-Glycinebetaine also protected the D1/D2/Cytb559 complexes against strong light-induced damage to the photochemical reactions and the irreversible bleaching of beta-carotene and chlorophyll. The presence of glycinebetaine also enhanced thermotolerance of the D1/D2/Cytb559 complexes isolated in the presence of 1.0 mol/L betaine with an increase in the temperature for 50% inactivation from 29 degrees C to 35 degrees C. The results indicate an increased supramolecular structural stability in the presence of glycinebetaine.

The Z-scheme--down hill all the way.

The Z-scheme is considered in the context of personal recollections of events during the time that it was conceived and an evaluation of its enduring importance.

Lack of demonstratable effects of pollutants on cyt b sequences in wood ducks from a contaminated nuclear reactor cooling pond.

The effects of low levels of radiation on DNA mutation rates are largely unknown for free-living vertebrates. In this study we investigated the effects of contamination from cooling ponds at a nuclear production facility in South Carolina on the mutation rates in mitochondrial DNA in wood ducks (Aix sponsa). Specifically, we sequenced a 433-bp portion of the cytochrome b gene from 18 female-offspring pairs of wood ducks from contaminated ponds and 2 female-offspring pairs from control ponds. Very low haplotype diversity was observed overall, and no case of mutation between female and offspring could be satisfactorily documented. This suggests that the levels of radioactive contamination in these cooling ponds have little effect on the mutation rate of mitochondrial DNA in these waterfowl and that mitochondrial DNA may not be as sensitive an indicator as previously anticipated.

Characterization of the light-induced cross-linking of the alpha-subunit of cytochrome b559 and the D1 protein in isolated photosystem II reaction centers.

Illumination of the isolated reaction center of photosystem II generates a protein of 41 kDa molecular mass. Using immunoblotting, it is confirmed that the protein is an adduct of the D1 protein and the alpha-subunit of cytochrome b559. Its formation seems to be photochemically induced, being independent of temperature between 4 and 20 degrees C and unaffected by a mixture of protease inhibitors. The maximum levels are detected when the pH is in the region 6.5-8.5 and when illumination intensities are moderate. Although higher light intensities induce a higher rate of formation, the accumulation of elevated levels of the 41-kDa protein does not occur due to light-induced degradation. This degradation is also unaffected by the presence of protease inhibitors. Proteolytic mapping and N-terminal sequencing indicates that the cross-linking process involves the N-terminal serine of the alpha-subunit of cytochrome b559 and D1 residues in the 239-244 FGQEEE motif close to the QB binding site. In conclusion, the results indicate that the N terminus of the alpha-subunit is exposed on the stromal side of photosystem II in such a way as to undergo light-induced cross-linking in the QB region of the D1 protein. They also suggest that the 41-kDa adduct may be an intermediate before the light-induced cleavage of the D1 protein in the FGQEEE region.

Magnetic circular dichroism study of cytochrome ba3 from Thermus thermophilus: spectral contributions from cytochromes b and a3 and nanosecond spectroscopy of CO photodissociation intermediates.

Near-UV-vis magnetic and natural circular dichroism (MCD and CD) spectra of oxidized, reduced, and carbonmonoxy-complexed cytochrome ba3, a terminal oxidase from the bacterium Thermus thermophilus, and nanosecond time-resolved MCD (TRMCD) and CD (TRCD) spectra of the unligated species formed after photodissociation of the CO complex are presented. The spectral contributions of individual cytochromes b and a3 to the Soret region MCD are identified. TRMCD spectroscopy is used to follow the spin state change (S = 0 to S = 2) in cytochrome a3(2+) following photodissociation of the CO complex. There is prompt appearance of the high-spin state after photolysis, as found previously in mammalian cytochrome oxidase [Goldbeck, R. A., Dawes, T. D., Einarsdóttir, O., Woodruff, W. H., & Kliger, D. S. (1991) Biophys. J. 60, 125-134]. Peak shifts of 1-10 nm appear in the TRMCD, TRCD, and time-resolved UV-vis absorption spectra of the photolyzed enzyme throughout its observable lifetime, indicating that the photolyzed enzyme does not relax to its equilibrium deliganded form before recombination with CO occurs hundreds of milliseconds later. Direct heme-heme interaction is not found in cytochrome ba3, but red-shifts in the MCD and absorption spectra of both cytochromes b and (photolyzed) a3 are correlated with a CO-liganded form of the protein. The long time (tau approximately greater than 1 s) needed for relaxation of the cytochrome b and a3 peaks to their static positions suggests that CO binding to a3 induces a global conformational change in the protein that weakly perturbs the MCD and absorption spectra of b and photolyzed a3. Fea3 binds CO more weakly in cytochrome ba3 than in cytochrome aa3. The MCD spectrum of reduced enzyme solution placed under 1 atm of CO contains a peak at 446 nm that shows approximately 30% of total cytochrome a3 remains pentacoordinate, high-spin.

Characterization of a 41 kDa photoinhibition adduct in isolated photosystem II reaction centres.

When isolated reaction centres of photosystem II are subjected to photoinhibitory illumination, a 41 kDa SDS-PAGE band is observed under all experimental conditions. The same band is also found, together with lower molecular weight fragments of the D1 protein, in whole thylakoids and in all PSII sub-particles investigated up to now. In the case of isolated reaction centres the 41 kDa band is represented by a heterodimer of the D1 polypeptide and the alpha-subunit of cytochrome b559. The cross-linkage between D1 and alpha-cyt b559 involves a region on D1 between the N-terminal residue and Arg-225, and is an early event in photo-induced damage to the D1 protein.

A photo-chemically induced dynamic nuclear polarization NMR study on rabbit and bovine cytochrome b5.

Although it has been indicated that proteins with chromophoric groups are not suitable for photo-chemically induced dynamic nuclear polarization (photo-CIDNP) measurements, we have successfully obtained these spectra for a heme protein, cytochrome b5. The characteristics of the spectra differed in some points from those so far reported. The intensities of the signals in the aromatic region were very weak, while those of the beta-methylene protons of one histidine and one tryptophan were extremely strong in comparison with the aromatic protons. It was demonstrated, on the basis of the photo-CIDNP spectrum, that one of seven histidines, all three tyrosines and a single tryptophan of the rabbit soluble cytochrome b5 are exposed on the surface of the protein. The results of comparison of the photo-CIDNP spectra for the rabbit soluble and intact, and bovine intact, cytochrome b5 led us to the conclusion that the conformation of the hydrophilic, catalytic part of cytochrome b5 is quite similar among these three proteins. In the presence of Chaps micelles, bovine intact cytochrome b5 was in monomeric form and the histidine signals disappeared from its photo-CIDNP spectrum. When bovine intact cytochrome b5 was reconstituted into egg yolk phosphatidylcholine liposomes, although separate signals due to the protein part were observed in the normal 1H-NMR spectrum, no photo-CIDNP signal could be detected. The normal spectrum suggests that the conformation of the protein embedded in liposomes is similar to that of the oligomeric form without lipids or a detergent.

Target inactivation analysis applied to determination of molecular weights of rat liver proteins in the purified state and in microsomal membranes.

In principle, target inactivation analysis provides a means of determining the molecular weights (Mr) and states of aggregation of proteins in native environments where they are functionally active. We applied this irradiation technique to the rat liver microsomal membrane proteins: cytochrome b5, epoxide hydrolase, flavin-containing monooxygenase, NADH-ferricyanide reductase, NADPH-cytochrome P-450 reductase, and seven different forms of cytochrome P-450. Catalytic activities, spectral analysis of prosthetic groups, and sodium dodecyl sulfate-polyacrylamide electrophoresis/peroxidase-coupled immunoblotting were used to estimate apparent Mr values in rat liver microsomal membranes. Except in one case (cytochrome P-450PCN-E), the estimated Mr corresponded most closely to that of a monomer. Purified cytochrome P-450PB-B, NADPH-cytochrome P-450 reductase and epoxide hydrolase were also subjected to target inactivation analysis, and the results also suggested monomeric structures for all three proteins under these conditions. However, previous hydrodynamic and gel-exclusion results clearly indicate that all three of these proteins are oligomeric under these conditions. The discrepancy between target inactivation Mr estimates and hydrodynamic results is attributed to a lack of energy transfer between monomeric units. Thus, while P-450PCN-E may be oligomeric in microsomal membranes, target inactivation analysis does not appear to give conclusive results regarding the states of aggregation of these microsomal proteins.