Probing molecular interactions of semiquinone radicals at quinone reduction sites of cytochrome bc1 by X-band HYSCORE EPR spectroscopy and quantum mechanical calculations

Quinone redox reactions involve a semiquinone (SQ) intermediate state. The catalytic sites in enzymes stabilize the SQ state via various molecular interactions, such as hydrogen bonding to oxygens of the two carbonyls of the benzoquinone ring. To understand how these interactions contribute to SQ stabilization, we examined SQ in the quinone reduction site (Qi) of cytochrome bc1 using electron paramagnetic resonance (ESEEM, HYSCORE) at the X-band and quantum mechanical (QM) calculations. We compared native enzyme (WT) with a H217R mutant (replacement of histidine that interacts with one carbonyl of the occupant of Qi to arginine) in which the SQ stability has previously been shown to markedly increase. The 14N region of the HYSCORE 2D spectrum for SQi in WT had a shape typical of histidine residue, while in H217R, the spectrum shape changed significantly and appeared similar to the pattern described for SQ liganded natively by arginine in cytochrome bo3. Parametrization of hyperfine and quadrupolar interactions of SQi with surrounding magnetic nuclei (1H, 14N) allowed us to assign specific nitrogens of H217 or R217 as ligands of SQi in WT and H217R, respectively. This was further substantiated by qualitative agreement between the experimental (EPR-derived) and theoretical (QM-derived) parameters. The proton (1H) region of the HYSCORE spectrum in both WT and H217R was very similar and indicative of interactions with two protons, which in view of the QM calculations, were identified as directly involved in the formation of a H-bond with the two carbonyl oxygens of SQ (interaction of H217 or R217 with O4 and D252 with O1). In view of these assignments, we explain how different SQ ligands effectively influence SQ stability. We also propose that the characteristic X-band HYSCORE pattern and parameters of H217R are highly specific to the interaction of SQ with the nitrogen of arginine. These features can thus be considered as potential markers of the interaction of arginine with SQ in other proteins.

Low-cost stopped-flow and freeze-quench device for double mixing

Experiments based on fast reagent mixing and observation of reaction progress are considered a powerful tool for investigating the kinetics of chemical and enzymatic reactions. Various spectroscopic methods are used in monitoring the reaction progress, which require different sample preparation methods. Stopped-flow is the most widespread method, where the reaction in the liquid phase is observed by optical absorption spectroscopy. Albeit less popular, the freeze-quench method is also used, in which the reaction is rapidly stopped by freezing the sample at a given time point after the reaction onset. The frozen droplets of the sample are collected and measured at low temperatures in the solid state. Currently, many commercial solutions are available for freeze-quench or stopped-flow experiments, but despite the high price of the devices, most of these do not allow combining both these methods in a single experiment. This study presents a relatively simple solution that combines both these methods, thus making a complete study of chemical or enzymatic reactions possible. Besides, the presented solution enables sequential double mixing of reagents, which is generally problematic and cannot be done using commercial instruments.

High-resolution cryo-EM structures of plant cytochrome b6f at work

Plants use solar energy to power cellular metabolism. The oxidation of plastoquinol and reduction of plastocyanin by cytochrome b₆f (Cyt b₆f) is known as one of the key steps of photosynthesis, but the catalytic mechanism in the plastoquinone oxidation site (Q_p) remains elusive. Here, we describe two high-resolution cryo-EM structures of the spinach Cyt b₆f homodimer with endogenous plastoquinones and in complex with plastocyanin. Three plastoquinones are visible and line up one after another head to tail near Q_p in both monomers, indicating the existence of a channel in each monomer. Therefore, quinones appear to flow through Cyt b₆f in one direction, transiently exposing the redox-active ring of quinone during catalysis. Our work proposes an unprecedented one-way traffic model that explains efficient quinol oxidation during photosynthesis and respiration.

Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes

This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.

A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice

We previously observed an unexpected fivefold (35 vs. 200 days) difference in the survival of respiratory chain complex III (CIII) deficient Bcs1l^p.S78G mice between two congenic backgrounds. Here, we identify a spontaneous homoplasmic mtDNA variant (m.G14904A, mt-Cyb^p.D254N), affecting the CIII subunit cytochrome b (MT-CYB), in the background with short survival. We utilize maternal inheritance of mtDNA to confirm this as the causative variant and show that it further decreases the low CIII activity in Bcs1l^p.S78G tissues to below survival threshold by 35 days of age. Molecular dynamics simulations predict D254N to restrict the flexibility of MT-CYB ef loop, potentially affecting RISP dynamics. In Rhodobacter cytochrome bc₁ complex the equivalent substitution causes a kinetics defect with longer occupancy of RISP head domain towards the quinol oxidation site. These findings represent a unique case of spontaneous mitonuclear epistasis and highlight the role of mtDNA variation as modifier of mitochondrial disease phenotypes.

Distinct properties of semiquinone species detected at the ubiquinol oxidation Qo site of cytochrome bc1 and their mechanistic implications

The two-electron ubiquinol oxidation or ubiquinone reduction typically involves semiquinone (SQ) intermediates. Natural engineering of ubiquinone binding sites of bioenergetic enzymes secures that SQ is sufficiently stabilized, so that it does not leave the site to membranous environment before full oxidation/reduction is completed. The ubiquinol oxidation Q_o site of cytochrome bc₁ (mitochondrial complex III, cytochrome b₆f in plants) has been considered an exception with catalytic reactions assumed to involve highly unstable SQ or not to involve any SQ intermediate. This view seemed consistent with long-standing difficulty in detecting any reaction intermediates at the Q_o site. New perspective on this issue is now offered by recent, independent reports on detection of SQ in this site. Each of the described SQs seems to have different spectroscopic properties leaving space for various interpretations and mechanistic considerations. Here, we comparatively reflect on those properties and their consequences on the SQ stabilization, the involvement of SQ in catalytic reactions, including proton transfers, and the reactivity of SQ with oxygen associated with superoxide generation activity of the Q_o site.

Effect of H bond removal and changes in the position of the iron-sulphur head domain on the spin-lattice relaxation properties of the [2Fe-2S](2+) Rieske cluster in cytochrome bc(1)

Here, comparative electron spin–lattice relaxation studies of the 2Fe–2S iron–sulphur (Fe–S) cluster embedded in a large membrane protein complex – cytochrome bc₁ – are reported.

Here, comparative electron spin–lattice relaxation studies of the 2Fe–2S iron–sulphur (Fe–S) cluster embedded in a large membrane protein complex – cytochrome bc₁ – are reported. Structural modifications of the local environment alone (mutations S158A and Y160W removing specific H bonds between Fe–S and amino acid side chains) or in combination with changes in global protein conformation (mutations/inhibitors changing the position of the Fe–S binding domain within the protein complex) resulted in different redox potentials as well as g-, g-strain and the relaxation rates (T₁^–1) for the Fe–S cluster. The relaxation rates for T < 25 K were measured directly by inversion recovery, while for T > 60 K they were deduced from simulation of continuous wave EPR spectra of the cluster using a model that included anisotropy of Lorentzian broadening. In all cases, the relaxation rate involved contributions from direct, second-order Raman and Orbach processes, each dominating over different temperature ranges. The analysis of T₁^–1 (T) over the range 5–120 K yielded the values of the Orbach energy (E_Orb), Debye temperature θ_D and Raman process efficiency C_Ram for each variant of the protein. As the Orbach energy was generally higher for mutants S158A and Y160W, compared to wild-type protein (WT), it is suggested that H bond removal influences the geometry leading to increased strength of antiferromagnetic coupling between two Fe ions of the cluster. While θ_D was similar for all variants (∼107 K), the efficiency of the Raman process generally depends on the spin–orbit coupling that is lower for S158A and Y160W mutants, when compared to the WT. However, in several cases C_Ram did not only correlate with spin–orbit coupling but was also influenced by other factors – possibly the modification of protein rigidity and therefore the vibrational modes around the Fe–S cluster that change upon the movement of the iron–sulphur head domain.

Mitochondrial Disease-related Mutation G167P in Cytochrome b of Rhodobacter capsulatus Cytochrome bc1 (S151P in Human) Affects the Equilibrium Distribution of [2Fe-2S] Cluster and Generation of Superoxide

Cytochrome bc₁ is one of the key enzymes of many bioenergetic systems. Its operation involves a large scale movement of a head domain of iron-sulfur protein (ISP-HD), which functionally connects the catalytic quinol oxidation Q_o site in cytochrome b with cytochrome c₁. The Q_o site under certain conditions can generate reactive oxygen species in the reaction scheme depending on the actual position of ISP-HD in respect to the Q_o site. Here, using a bacterial system, we show that mutation G167P in cytochrome b shifts the equilibrium distribution of ISP-HD toward positions remote from the Q_o site. This renders cytochrome bc₁ non-functional in vivo. This effect is remediated by addition of alanine insertions (1Ala and 2Ala) in the neck region of the ISP subunit. These insertions, which on their own shift the equilibrium distribution of ISP-HD in the opposite direction (i.e. toward the Q_o site), also act in this manner in the presence of G167P. Changes in the equilibrium distribution of ISP-HD in G167P lead to an increased propensity of cytochrome bc₁ to generate superoxide, which becomes evident when the concentration of quinone increases. This result corroborates the recently proposed model in which “semireverse” electron transfer back to the Q_o site, occurring when ISP-HD is remote from the site, favors reactive oxygen species production. G167P suggests possible molecular effects of S151P (corresponding in sequence to G167P) identified as a mitochondrial disease-related mutation in human cytochrome b. These effects may be valid for other human mutations that change the equilibrium distribution of ISP-HD in a manner similar to G167P.

Molecular organization of cytochrome c2 near the binding domain of cytochrome bc1 studied by electron spin-lattice relaxation enhancement

Measurements of specific interactions between proteins are challenging. In redox systems, interactions involve surfaces near the attachment sites of cofactors engaged in interprotein electron transfer (ET). Here we analyzed binding of cytochrome c₂ to cytochrome bc₁ by measuring paramagnetic relaxation enhancement (PRE) of spin label (SL) attached to cytochrome c₂. PRE was exclusively induced by the iron atom of heme c₁ of cytochrome bc₁, which guaranteed that only the configurations with SL to heme c₁ distances up to ∼30 Å were detected. Changes in PRE were used to qualitatively and quantitatively characterize the binding. Our data suggest that at low ionic strength and under an excess of cytochrome c₂ over cytochrome bc₁, several cytochrome c₂ molecules gather near the binding domain forming a “cloud” of molecules. When the cytochrome bc₁ concentration increases, the cloud disperses to populate additional available binding domains. An increase in ionic strength weakens the attractive forces and the average distance between cytochrome c₂ and cytochrome bc₁ increases. The spatial arrangement of the protein complex at various ionic strengths is different. Above 150 mM NaCl the lifetime of the complexes becomes so short that they are undetectable. All together the results indicate that cytochrome c₂ molecules, over the range of salt concentration encompassing physiological ionic strength, do not form stable, long-lived complexes but rather constantly collide with the surface of cytochrome bc₁ and ET takes place coincidentally with one of these collisions.

Thalidomide and chemotherapy combination

Angiogenesis has been shown to be important in tumor growth and metastasis. Thalidomide, an oral sedative, has recently been found to inhibit angiogenesis. We therefore set out to ask whether thalidomide can be used as therapy for breast cancer. In a mouse model of breast cancer, we found that thalidomide alone did not suppress tumor growth. However, mice treated with thalidomide in combination with cytoxan and adriamycin had significantly smaller tumors than those given the two chemotherapeutic agents alone (3,432 +/- 303 mm(3) versus 4,643 +/- 203 mm(3), p = 0.0005). We proceeded to administer thalidomide together with chemotherapy to seven breast cancer patients in the context of a Phase I trial. Side effects attributed to thalidomide were minimal, and included constipation and a rash. We concluded that an approach at cancer therapeutics combining an antiangiogenic agent such as thalidomide with conventional chemotherapy may be feasible and deserves further studies.

Reorientation of cytochrome c2 upon interaction with oppositely charged macromolecules probed by SR EPR: implications for the role of dipole moment to facilitate collisions in proper configuration for electron transfer

The reaction of water-soluble cytochrome c (c(2)) with its physiological redox partners is facilitated by electrostatic attractions between the two protein surfaces. Using spin-labeled cytochrome c(2) from Rhodobacter capsulatus and pulse electron paramagnetic resonance (EPR) measurements we compared spatial orientation of cytochrome c(2) upon its binding to surfaces of opposite charge. We observed that cytochrome c(2) can use its negatively charged "back" side when exposed to interact with positively charged surfaces (DEAE resin) which is the opposite to the use of its positively charged "front" side in physiological interaction with negatively charged binding domain of cytochrome bc(1). The later orientation is also adopted upon non-physiological binding of cytochrome c(2) to negatively charged carboxymethyl cellulose resin. These results directly demonstrate how the electric dipolar nature of cytochrome c(2) influences its orientation in interactions with charged surfaces, which may facilitate collisions with other redox proteins in a proper orientation to support physiologically-competent electron transfer. Saturation recovery EPR provides an attractive tool for monitoring spatial orientation of proteins in their interaction with surfaces in liquid phase. It is particularly valuable for metalloproteins engaged in redox reactions as a means to monitor the geometry and dynamics of formation of protein complexes in measurements that are independent of electron transfer processes.

Inhibitory effects of combinations of HER-2/neu antibody and chemotherapeutic agents used for treatment of human breast cancers

Previous studies have demonstrated a synergistic interaction between rhuMAb HER2 and the cytotoxic drug cisplatin in human breast and ovarian cancer cells. To define the nature of the interaction between rhuMAb HER2 and other classes of cytotoxic drugs, we applied multiple drug effect/combination index (CI) isobologram analysis to a variety of chemotherapeutic drug/rhuMAb HER2 combinations in vitro. Synergistic interactions at clinically relevant drug concentrations were observed for rhuMAb HER2 in combination with cisplatin (CI=0.48, P=0.003), thiotepa (CI=0.67, P=0.0008), and etoposide (CI=0.54, P=0.0003). Additive cytotoxic effects were observed with rhuMAb HER2 plus doxorubicin (CI=1.16, P=0.13), paclitaxel (CI=0.91, P=0.21), methotrexate (CI=1.15, P=0.28), and vinblastine (CI=1.09, P=0.26). One drug, 5-fluorouracil, was found to be antagonistic with rhuMAb HER2 in vitro (CI=2.87, P=0.0001). In vivo drug/rhuMAb HER2 studies were conducted with HER-2/neu-transfected, MCF7 human breast cancer xenografts in athymic mice. Combinations of rhuMAb HER2 plus cyclophosphamide, doxorubicin, paclitaxel, methotrexate, etoposide, and vinblastine in vivo resulted in a significant reduction in xenograft volume compared to chemotherapy alone (P<0.05). Xenografts treated with rhuMAb HER2 plus 5-fluorouracil were not significantly different from 5-fluorouracil alone controls consistent with the subadditive effects observed with this combination in vitro. The synergistic interaction of rhuMAb HER2 with alkylating agents, platinum analogs and topoisomerase II inhibitors, as well as the additive interaction with taxanes, anthracyclines and some antimetabolites in HER-2/neu-overexpressing breast cancer cells demonstrates that these are rational combinations to test in human clinical trials.

Detection and quantification of regional wall motion abnormalities using phase analysis of equilibrium gated cardiac studies

Phase images obtained from equilibrium gated cardiac studies were evaluated for qualitative and quantitative information and correlated with contrast angiography in 33 patients. The left ventricular region of interest was obtained by a semiautomatic procedure which avoided underestimation of size but also eliminated extraventricular pixels. Phase images and phase distribution histograms were arranged in three standard displays which included the whole heart, isolated left ventricle, isolated abnormal areas, and quantification of maximum phase shift in the whole free border and in the inferolateral and posterolateral segments. Only the free left ventricular border was evaluated. According to contrast angiography results, four categories were obtained: normal, hypokinetic, akinetic, and dyskinetic. The best correlation with contrast angiography was found with the results obtained by dividing the left ventricular free border in two segments (r = 0.91). Scheffe's test for multiple comparisons showed significant differences between each of the four categories. Expressed in phase shifts from the histogram mode, the lower limits for the three abnormal categories were established at 30 degrees, 78 degrees, and 156 degrees respectively for hypokinetic, akinetic, and dyskinetic segments. For distinguishing normal from abnormal segments, sensitivity = 83%, specificity = 94%, and accuracy = 89%. The main reasons for discrepant results appeared to be small hypokinetic areas in an otherwise normal ventricle, very large area of hypokinesia, segments adjacent to an area of marked abnormality, and ventricles with asynchrony (wave-like motion). The method described provides an image which characterizes myocardial synchrony, generates clear boundaries for abnormal areas, and lends itself to quantification.

Angiographic correlates of recurrent sustained ventricular tachycardia in chronic ischemic heart disease

We report the angiographic studies of 53 consecutive patients with angiographic coronary artery disease (CAD) and recurrent sustained ventricular tachycardia occurring at least 6 weeks remote from an acute myocardial infarction. Triple-vessel disease was present in 25 patients (47%), double-vessel disease in 19 patients (36%), and single-vessel disease in nine patients (17%). All patients with single-vessel disease had left anterior descending coronary artery obstruction. Patients under 50 years old had significantly fewer diseased vessels than those over 50 years old (1.4 vs 2.4 vessels diseased; p less than 0.025). Left ventricular ejection fraction ranged from 0.15 to 0.61 (mean 0.34 +/- 0.11) and was 0.25 or less in 14 patients (26%). All patients had regional wall motion abnormalities. There was akinesia and/or dyskinesia in 49 patients (92%). Akinesia or dyskinesia was inferior in 17 patients (32%), anteroapical in 14 patients (26%), inferoapical in 10 patients (19%), and anteroapicoinferior in 6 patients (11%). Involvement of the septum was noted in 19 patients (36%) and of basal segments in 26 patients (49%). An average of 2.7 (out of seven) segments per patient were dyskinetic or akinetic. Thus multivessel disease, markedly reduced ejection fraction, and severe and extensive regional wall motion abnormalities are generally present. These findings have pathophysiologic as well as clinical and therapeutic implications. The nautral history of these patients as well as the results of therapy should be related to the underlying coronary anatomy and left ventricular function.

Equilibrium radionuclide gated angiography in patients with tricuspid regurgitation

Equilibrium gated radionuclide angiography was performed in 2 control groups (15 patients with no organic heart disease and 24 patients with organic heart disease but without right- or left-sided valvular regurgitation) and in 9 patients with clinical tricuspid regurgitation. The regurgitant index, or ratio of left to right ventricular stroke counts, was significantly lower in patients with tricuspid regurgitation than in either control group (range and mean +/- standard error of the mean 0.4 to 1.0, 0.7 +/- 0.1 versus 1.0 to 1.5, 1.3 +/- 0.1 and 1.0 to 2.9, 1.5 +/- 0.1, respectively, p less than 0.001). Time-activity variation over the liver was used to compute a hepatic expansion fraction which was significantly higher in patients with tricuspid regurgitation than in either control group (1.4 to 11.4, 5.8 +/- 1.0% versus 0.6 to 3.4, 1.9 +/- 0.3% and 1.0 to 5.1, 2.3 +/- 0.2%, respectively, p less than 0.001). Fourier analysis of time-activity variation in each pixel was used to generate amplitude and phase images. Only pixels with values for amplitude at least 7% of the maximum in the image were retained in the final display. All patients with tricuspid regurgitation had greater than 100 pixels over the liver automatically retained by the computer. These pixels were of phase comparable to that of the right atrium and approximately 180 degrees out of phase with the right ventricle. In contrast, no patient with no organic heart disease and only 1 of 24 patients with organic heart disease had any pixels retained by the computer. In conclusion, patients with tricuspid regurgitation were characterized on equilibrium gated angiography by an abnormally low regurgitant index (7 of 9 patients) reflecting increased right ventricular stroke volume, increased hepatic expansion fraction (7 of 9 patients), and increased amplitude of count variation over the liver in phase with the right atrium (9 of 9 patients).

Tricuspid insufficiency detected by equilibrium gated radionuclide study

The results of a gated radionuclide cardiac study are reported in a patient with biventricular failure and tricuspid insufficiency demonstrated by clinical evaluation, M-mode and 2-D sector echocardiography, and cardia catheterization. The processed gated radionuclide cardiac study showed a left ventricular/right ventricular stroke volume ratio of 0.5; expansion of the hepatic blood pool demonstrated by hepatic time activity curve and calculation of an "'expansion fraction"; and synchronous changes of count rate of the atrial and hepatic regions detected by phase analysis (similar phase shifts).

Assessment of left ventricular function by radionuclide angiography during induced supraventricular tachycardia

Electrocardiographically synchronized radionuclide angiography was performed before, during and after induced paroxysmal supraventricular tachycardia in 13 patients. Data were acquired with a computer-interfaced Anger camera in a left anterior oblique projection. No data were acquired during tachycardia until tachycardia had been sustained for 1 minute. Patients ranged in age from 20 to 64 years (mean +/- standard deviation 42 +/- 14.5). Three patients had organic heart disease and 10 did not. Baseline and tachycardia heart rates (beats/min) were 59 to 99 (73 +/- 11) versus 141 to 228 (157 +/- 22). Baseline and tachycardia left ventricular measurements (mean +/- standard error) were as follows: ejection fraction 64 +/- 2 versus 62 +/- 4 percent (not significant), ejection rate 3.0 +/- 0.1 versus 4.3 +/- 0.4 mean ventricular counts/s (p less than 0.001), normalized end-diastolic counts 72.7 +/- 7.8 versus 48.7 +/- 6.7 X 10(3) counts (p less than 0.001), normalized stroke counts 37.1 +/- 3.4 versus 23.3 +/- 2.7 X 10(3) counts (p less than 0.001) and normalized count cardiac output 2,717.5 +/- 273.0 versus 3,620.2 +/- 403.7 X 10(3) counts/min (p less than 0.005). Although ejection fraction for the whole group did not change significantly, it decreased during tachycardia by 5 percentage points or more in five patients. These were the three patients with heart disease and the two normal patients with the fastest heart rate during tachycardia (228 and 214 beats/min, respectively). In summary, paroxysmal supraventricular tachycardia was characterized by a marked decrease in left ventricular end-diastolic and stroke volumes but increased ejection rate and cardiac output without significant change in ejection fraction. Heart disease or rapid heart rate during tachycardia appeared to have a deleterious effect on ejection fraction.